DOVER — The City Council met in a workshop session Wednesday evening with New Hampshire Department of Environmental Services Commissioner Thomas Burack and his team to discuss the water quality issues in the Great Bay Estuary.

The session, set up through state Sen. David Watters, was used for councilors to ask questions they had about the permit the city will be receiving in the next two years that calls for the city to limit the amount of nitrogen in the estuary significantly and pay millions of dollars to update its wastewater treatment facility in order to do so.

Burack began the meeting discussing his agency’s position on the bill Sen. Watters created, SB110, that assists in resolving the questions that continue to be asked regarding the Great Bay as an impaired body of water.

He said the bill asks for NHDES to engage in both adopting the rules of numeric criteria 2009 and to submit the rules in the study for an independent peer review. He said this study was done almost five years ago and none of the numbers in the document were ever enforced on any entity and that reviewing it again would not be worth it because of its age.

“NHDES would like to work with you to design a program,” he said, but that time would not be well spent re-reviewing the study, which had been reviewed by two independent experts in 2010.

Between many questions, Burack continued to state that he believes the work that needs to be done to answer questions and prepare the city for the permit should be done together and that the council should work with NHDES to determine which questions needs to go to which departments, NHDES, attorneys or the Environmental Protection Agency.

“What we really hope for is a constructive partnership in the years ahead,” he said, later adding, “ I can’t help but believe we want to work together.”

Deputy Mayor Robert Carrier said the council agrees they need to clean up the environment.

“It’s unfortunate that many years ago we were so sloppy,” he said. “And now we want to clean up our mess.”

Burack spent a majority of the session listening to the concerns of the councilors, one in particular being the cost of the permit.

“We’re here and we have to explain to our taxpayers why their sewer bill has just gone sky high,” Councilor Dorothea Hooper said.

“Dover has a unique situation as compared to Newmarket and Exeter,” he said about two other towns who have already received their permit. “We’re a different situation.”

Dover has an updated wastewater treatment plant, but will need to update it again in order to bring nitrogen levels down from their current 15 to 20 milligrams per liter to 3 milligrams per liter.

Burack said that the cost of the update is high, but to imagine a life without clean water.

“We would not have the quality of life that we have here,” he said.

Burack suggested to the council that they work together and come up with lists of questions and establish steps in order to seek what data would be most helpful before the permit for the city is received.

Another meeting between both the City and NHDES was not scheduled, but Sen. Watters said his bill will be coming up for a hearing in two and a half weeks.